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While large-scale genomic approaches are increasingly revealing the genetic basis of polymorphic phenotypes such as colour morphs, such approaches are almost exclusively conducted in species with high-quality genomes and annotations. Here, we use Pool-Seq data for both genome assembly and SNP frequency estimation, followed by scanning for F ST outliers to identify divergent genomic regions. Using paired-end, short-read sequencing data from two groups of individuals expressing divergent phenotypes, we generate a de novo rough-draft genome, identify SNPs and calculate genomewide F ST differences between phenotypic groups. As genomes generated by Pool-Seq data are highly fragmented, we also present an approach for super-scaffolding contigs using existing protein-coding data sets. Using this approach, we reanalysed genomic data from two recent studies of birds and butterflies investigating colour pattern variation and replicated their core findings, demonstrating the accuracy and power of a Pool-Seq-only approach. Additionally, we discovered new regions of high divergence and new annotations that together suggest novel parallels between birds and butterflies in the origins of their colour pattern variation., (© 2017 John Wiley & Sons Ltd.)

Discovering cryptic species in well-studied areas and taxonomic groups can have profound implications in understanding eco-evolutionary processes and in nature conservation because such groups often involve research models and act as flagship taxa for nature management. In this study, we use an array of techniques to study the butterflies in the Spialia sertorius species group (Lepidoptera, Hesperiidae). The integration of genetic, chemical, cytogenetic, morphological, ecological and microbiological data indicates that the sertorius species complex includes at least five species that differentiated during the last three million years. As a result, we propose the restitution of the species status for two taxa often treated as subspecies, Spialia ali (Oberthür, 1881) stat. rest. and Spialia therapne (Rambur, 1832) stat. rest., and describe a new cryptic species Spialia rosae Hernández-Roldán, Dapporto, Dincă, Vicente & Vila sp. nov. Spialia sertorius (Hoffmannsegg, 1804) and S. rosae are sympatric and synmorphic, but show constant differences in mitochondrial DNA, chemical profiles and ecology, suggesting that S. rosae represents a case of ecological speciation involving larval host plant and altitudinal shift, and apparently associated with Wolbachia infection. This study exemplifies how a multidisciplinary approach can reveal elusive cases of hidden diversity., (© 2016 John Wiley & Sons Ltd.)

Inherited bacteria are now recognized as important players in arthropod evolution and ecology. Here, we test spiders, a group recently identified as possessing inherited bacteria commonly, for the presence of two reproductive parasites, Cardinium hertigii (Bacteroidetes group) and Wolbachia (alpha-proteobacteria), estimating incidence, prevalence, any sex bias in infection, and infection diversity, for a panel of field-collected specimens. We identify spiders as a hotspot for Cardinium. Present in 22% of the sampled species, incidence was significantly higher than that previously recorded in insects. Where present, Cardinium infection occurred at medium prevalence without evidence of sex bias in prevalence that would indicate sex-ratio distortion activity. Wolbachia was present in 37% of species, but revealed a gradation from being rare to very common. In one case, Wolbachia was found significantly more commonly in females than males, indicating it may act as a sex-ratio distorter in some species. Breeding work conducted on two species confirmed that Wolbachia and Cardinium were transmitted maternally, which represents the first proof of inheritance of these symbionts in spiders. Overall, this study demonstrates that the majority of spider species are infected with inherited bacteria, and their role in host biology clearly requires determination.

Male-killing bacteria are generally thought to attain low to intermediate prevalence in natural populations, with only mild effects on the host population sex ratio. This view was recently challenged by reports of extremely high infection frequencies in three butterfly species, raising the prospect that male killers, by making males rare, might drive many features of host ecology and evolution. To assess this hypothesis, it is necessary to evaluate how often male killers actually produce a highly female-biased population sex ratio in nature, which requires both high prevalence of infection and high penetrance of action. To this end, we surveyed South Pacific and Southeast Asian populations of Hypolimnas bolina, a butterfly in which extreme prevalence of male-killing Wolbachia bacteria has recently been recorded. Our results indicate that highly female-biased populations are common in Polynesia, with 6 out of 12 populations studied having in excess of 70% of females infected with a fully efficient male killer. However, heterogeneity is extreme in Polynesia, with the male-killing Wolbachia absent from three populations. In contrast to the Polynesian situation, Wolbachia does not kill males in any of the three Southeast Asian populations studied, despite its very high prevalence there. We conclude that male killers are likely to have significant ongoing ecological and evolutionary impact in 6 of the 15 populations surveyed. The causes and consequences of the observed spatial variation are discussed with respect to host resistance evolution, host ecology and interference with additional symbionts.